The Stowaway
by Snazzy Pants
Summary: Samus knew that the Pirates were capable of great cruelty. But she never knew how intense this cruelty was until Maxis Reeve stowed away on her ship following a raid on a Pirate complex. Chapter 5 up! Rated M for certain suggestive scenes.
1. Chapter 1

I do not own Metroid, or the space pirates, or any of the trademarked names and places in this fanfic. They belong to Nintendo. But you already knew that, right?

Anyways, this follows the events of Metroid Fusion. After she destroyed the station, Samus was to be put on trial for treason. But because they wanted to keep the Metroid breeding a secret, the Galactic Fedearation was forced to drop the charges in exchange for Samus's word that she would never discuss what had happened on the station.

Adam, on the other hand, was transferred to another ship, and all memories of the incident erased. This story takes place a year afterwards.

* * *

**Chapter 1: The Stowaway**

It was dark and it was cramped. But the cargo compartment on this strange ship was definitely better then what Maxis was leaving behind.

He'd been on this world for the better part of a year, but he'd barely seen the sky once. He'd never been outside of the Space Pirate science facility on the surface of the planet.

He had a year's worth of scars, mental and physical, from the thing's they'd done to him. They'd exposed him to dozens of different chemicals, performed possibly hundreds of surgeries, and put him through "trials" which measured just how much pain a human body could take before it passed out.

He thought that he would be doomed to a life of torture in this god-forsaken place. Until she arrived. He knew she was female from the female pronouns that the Pirates used to describe her. They called her the Hunter. Whoever she was, she laid waste to the Pirate forces.

In the confusion, Maxis managed to steal a blaster from one of the corpses. It was designed for Pirate hands, so he resorted to using it as a bludgeoning weapon. He was surprised at how easily it crushed a Pirate's skull, but he wrote it off to the extra strength from the adrenaline.

He saw the Hunter's ship, and quickly darted aboard, just as the Hunter herself fled from the facility, massive explosions rocking the complex. Maxis hid himself in the cargo area, as the ship lifted off. As the adrenaline wore off, his body finally realized how exhausted it was. He leaned his head against a crate, and was asleep before he realized it, his hands still clutching the blaster.

_Meanwhile, in the ship's cockpit..._

"Samus?"

"Hmm?"

"I'm detecting a strange lifesign in the cargo area. It's human, but I'm picking a lot of anomalies," the computer said.

"What? How come we didn't detect it before?"

"It wasn't there before."

Samus let out a sigh, and got out of her chair. "Well, let's pay our stowaway a visit," she said, walking around to the back of the ship where the cargo area was located. She tapped a few buttons on the keypad, and the door slid open with a faint faint whirr. Tapping another pad on the wall of the cargo bay, the dim lights switched on, flooding the small area with illumination. Leaning against a cargo crater, and clutching a pirate-made blaster, was the sleeping form of Maxis. Most of his body was covered in a black bodysuit, save his head. His face was obscured by his shaggy, dirty hair.

"Rise and shine, stowaway," Samus said, poking him in the side with her foot.

He woke with a start, and scampered past her to the other side of the cargo bay. He had the blaster raised like a club, and was staring at Samus suspiciously. He began saying something in the pirate language. At first, Samus couldn't understand it, and then the ship's translators kicked in.

"-this real? Are you real? Or is this another test?" Maxis said.

"Test? What are you talking abou-" Samus stopped midsentence as the realization hit her. It was odd that a human was speaking the pirate language, but now she recognized the blaster as well. "Oh god..." she said, slightly shocked.

"Samus? What's the problem?"

"I think I know where our stowaway came from."

* * *

Well, that's Chapter 1 of my Metroid Fanfic. In the next few chapters, you'll find out more about just what was done to this man by the Space Pirates in the facility. Please Read and Review. 

Stay Snazzy!


	2. Chapter 2

Well, here's chapter 2! Now you'll find out a bit more about what happened to Maxis.

And while I may not own Metroid, Maxis is a character of my own creation.

* * *

**Chapter 2: Altered  
**

It took some convincing, but Samus finally managed to get Maxis to believe that this was real and not a test. With that done, it was a small matter to get him to hand over the weapon, and to coax him out of the cargo bay. Now, in the noticibly brighter light of the main part of the ship, Samus was able to get a good look at the stowaway.

What she saw shocked her as much as her earlier realization did. There were symmetrical patches of scales on his cheeks, hard and black, instead of soft pink skin. But his eyes were the most unnerving part. They were a burning red, and the pupils were slitted, reptillian. It was obvious that Maxis was not entirely human.

"What's your name?" Samus asked, looking him right in his strange eyes.

"Maxis Reeve," he said in a subdued tone, still speaking in the Pirate language.

"My name is Samus. Care to tel me what happened down there?" she said, though she already had a pretty good idea. She had seen the specimen tanks. She had some of the Pirate data.

"Things that would make your blood run cold," Maxis responded. He was nervous, though not as much as he'd been earlier. This feeling was a familiar one, one that had developed in his year in the facility. Paranoia kept you alive.

"Try me," Samus said. She might have had an idea of what had happened, but she wanted to hear it for herself.

Maxis looked at her strangely, and saw a spark of something familiar. Something told him that he could trust this person. And so he began to speak.

"We were test subjects for god knows what. They put us in tanks of liquid, and attached our bodies to dozens of wires and tubes. They pumped burning, glowing chemicals into our veins. Liquids that made our whole existence sear, and others that made us feel nothing at all. Other procedures were a lot more... invasive. I have the scars to prove it.

When we weren't being experimented on, we were locked in cells, barely given the essentials to survive. It was in these cells that I learned their language. When it's the only thing spoken to you, you pick up fast. At least now I can curse them in their own tongue," Maxis explained, the seething rage at what was done to him audible in his tone.

Samus wasn't surprised at what she heard. She knew that the pirates were capable of atrocities, Tallon IV had been a prime example of that. But she'd never spoken to a survivor of these atrocities.

"And then you came. And I was free," he finished. He looked at Samus, and the gratitude in his face spoke volumes.

Samus was taken aback by this. Despite regularly putting her life on the line, and probably saving the galaxy at least once, she never got so much as a "thank you". But this man, who she hadn't even intended to rescue, was looking at her like his savior.

"Maxis, I'd like to run a couple of tests on you. Is that okay?" she asked. She wanted to know exactly what had been done to him by the Pirates in the facility.

Maxis flinched slightly at the sound of "test". "What kind of tests?" he asked, shifting his weight. After what he'd been through, the word "test" would make anyone nervous. But, he still felt that he could trust this woman.

"Nothing invasive, don't worry. I'm just going to run a blood test and a bioscan. Alright?" Samus said, trying to reassure him. Part of her respected him. After enduring a year of the torments he described, this man had still maintained his sanity. That took a lot of strength.

Reluctantyl, Maxis agreed. Samus led him to the ship's medical bay, and told him to sit down on the table. "You'll need to remove your shirt. I can't take a blood sample through your sleeve," she explained. Maxis nodded. Reaching up to his neck, he undid the tiny clasps on either side, and the bodysuit simply split in half, down to the waist.

Samus had to stifle a gasp as she saw his upper body and torso. Nearly his entire back was covered in the same scales that she'd seen on his face, and the extended down the backs of his arms and hands. His hands themselves were claw-like in appearance, definitely sharper than normal human hands. The scales also covered most of his chest, but his stomach was exposed, revealing numerous scars of various sizes.

She was used to killing things. It was what she did. She had seen blood, and she had spilled blood. But she would never purposely do something like this. Something that would leave lasting marks.

Samus ran a hand down the scales on his arm, examining the texture. They were smooth, like a reptile's or a lizard's, but were obviously very tough. She raised the small needle to his arm, and extracted a blood sample from the veins. She then walked over to a nearby terminal, placed the vial of blood into a slot, and pressed a few buttons to begin analysis.

"Lie down. I'm going to do the bioscan now," she said, instructing him to lay back on the table. Maxis obeyed, and Samus tapped a few more keys. A screen of greenish light was projected at the foot of the table, and slowly moved it's way up past the top of Maxix's head. It winked off, and he sat up.

"Done," samus said, now waiting for the results to process. "You can put your shirt back on, you know," she added, noticing that the top half of Maxis's bodysuit still hanging limply around his waist.

"I've been wearing this for a year. You wouldn't want to wear it either," he replied, matter-of-factly.

"Fair point."

A beeping from the terminal told her that the results had been processed. She pressed a button, and they were displayed on a small screen set next to the keypad.

"Whoa."

This was the only word she uttered as she looked over the results. _This would certainly explain his appearance_, she thought to herself. _His genetic structure is a mess._

"What? What is it?" Maxis said, growing more agitated. He didn't like tests to begin with, and Samus's silence was just adding to that.

"Maxis, those chemicals did a lot more than just change your appearance. The blood tests were inconclusive about what they put in you, but whatever it was, it did a number on your DNA. It's in a state of flux," she explained.

"Flux? What does that mean?" Maxis said, the panic in his voice rising. Hearing that something had "done a number" on your DNA was not usually a good thing.

"It means you're still changing. Into what, I don't know, but for now you should-" She was cut off midsentence as the whole ship shook from some sort of impact. "Computer, what the hell just hit us!" she called out.

"Unknown. Trajectory indicates that it originated in the northern hemisphere of the planet. Shall I begin evasive manouvers?" the computer asked, it's voice calm.

"You should. Now get us out of-" Once again, she was cut off, buy this time by the screech of metal being sheared.

"Outer hull has been compromised. Suggest emergency landing," the computer's ever-calm voice said, barely audible over a wailing klaxon.

"Affirmative. Begin landing sequence!" Samus shouted over the din. She threw herself into the captain's chair, and strapped herself in. "Maxis, you might want to grab onto something bolted down," she said, as the ship began shaking violently from reentry. Maxis grabbed hold of one of the terminals, and held on, digging his claw-like hands into the metal.

Another shriek of rending metal, and the shaking intensified. "Warning. secondary and tertiary thrusters offline. ELS failure. Impact with surface imminent," the computer said.

Samus gritted her teeth as she stared out the viewscreen, and the tree-covered ground rushing to meet them.

There was a terrible noise, and the world seemed to stand still for a moment. The moment ended, and all went dark.

* * *

What was it that took down Samus's ship? What will happen to them? Find out in Chapter 3! 


	3. Chapter 3

Thanks for the great reviews! Anyways, in this chapter, Samus and co. will be checking damage, suiting up, and heading towards whatever shot them down.

* * *

**Chapter 3: Suiting Up and Setting Out**

Samus was the first to wake. She shook her heard, trying to clear her vision. The view screen in front of her was completely obscured by the mud and rock that had that the ship had plowed through upon landing. "Computer? Report," she said, unstrapping herself from the captain's chair.

"83 percent of ship systems are offline.  
Communications offline.  
Propulsion offline.  
Main hull compromised.  
Probability of manual repair negligible.  
Self repair of internal systems: 72 hours," the computer rattled off. There were times when Samus envied the computer, with its ability to be completely calm in any situation.

"Well, what is functional?" she demanded.

"Ration replication systems online.  
Secondary weapons operating at 82 percent capacity.  
Power Suit recharge system operation at 94 percent capacity."

"Great. Of all the systems on the ship, the goddamned vending machine is the only one unscathed," she remarked sarcastically. _Why was it always the snack machine that survived crashes? Speaking of surviving..._ she thought, getting out of the chair and looking around the wreckage of her ship. It had obviously seen better days, and the ship was definitely tilted at an odd angle. Storage bins were scattered on the floor, their contents strewn about. Parts of ceiling panel had fallen off, exposing broken wires, and a rather large hole had been torn in the side of the ship. "Hey, Maxis. You still alive?" she said, looking for the other passenger. She found the stowaway unconscious on the floor, near the terminal he'd grabbed onto. He had a gash in his forehead above his eye, and there was a smear of blood on the corner of the terminal. Within seconds, however, the wound closed, and began to scab over.

_Must be part of the mutations. At least he's not dead,_ she thought to herself.

As if on cue, Maxis began to stir. He groaned, rubbing his head with a scaled hand. "Egh... What happened?" he mumbled, still dizzy from the impact.

"We crashed, that's what happened. You still in one piece?" she asked.

"Yeah, I think so. You?" he responded, getting to his feet.

"I've survived worse," she said. "By the way, have you seen my helmet? I want to check out how much damage was done to the hull," she said, looking around.

"I think it's over there," Maxis responded, pointing to a glint of red underneath a large chunk of ceiling.

Without breaking a sweat, Samus grabbed the piece of metal (which weighed as much as she did), shoved it aside with one hand, and retrieved her helmet with the other. She heard the click as it snapped into place. Turning around, she strode over to the hole in the side of the ship, and climbed out. Maxis followed, wanting to examine the wreck for himself. Had he left a second later, Samus would have been the target of the spider-like robot. Instead, it leapt at Maxis, knocking him to the ground and attempting to slice into him with its large and extremely sharp mandibles. He held it away from his throat, which it was attempting to cut into, and rammed a clawed hand into the joint where metal head met body. With a scream of protest, the metal tore as Maxis pulled, separating the robot's head from its body.

The body's needle-like legs spasmed once, before curling up beneath it. The head clicked the mandibles together a few more times, still trying to get at Maxis, before he pulled out most of the circuitry that controlled it. The mandibles froze in mid-bite. With his hand still sticking through the spider's head, he found that he could control the mandibles via manual means, almost like one of those old prosthetic hands.

"Huh," he remarked looking at the weapon that he'd accidentally created.

Samus had watched the whole thing. "I think you just found what wrecked by engines," she said, scanning the mandibles of the spider head. They were monofilament blades, sharpened to the width of a single molecule, and capable of shearing through titanium like it was nothing. It would explain why the ship's secondary thrusters were cut neatly in two.

She walked back over to the hole in her ship, and poked her head in to talk to the computer. "Computer, how far from here did the attack originate?" she asked.

"Origin is approximately 2 kilometers northwest of current position."

"Alright then."

Turning on her heel, she set off in the indicated direction, leaving Maxis running to catch up. "Wait a minute! I'm coming with you," he said, still holding the remains of the robot.

"No, you're not. I work alone, and I'd prefer it if I don't have to cover someone else's ass," Samus replied.

"What, I'm just supposed to wait here? Did it occur to you that I might be useful? That's probably another pirate facility, and I understand the language. Besides, I try this thing out," Maxis said, motioning to the robot head.

Samus stared long and hard at the man standing before her. She sighed, and then- "I know I'm going to regret this later, but fine. Grab some proper clothing, grab a shield, and grab a gun. But you'd better keep up. If I have to save your ass, I'll probably shoot you myself," Samus said tersely.

Maxis nodded, and headed back to the ship to get the aforementioned items. The shield she was referring to was a portable shield generator. It was similar in construction to the one in her suit, but nowhere near as powerful. It could defend against maybe three or four shots, but that was it. The clothing was simply a padded vest, and a pair of pants constructed from a rather tough material. Using a cutting torch that was miraculously spared from the crash, he sliced the spider body in half, and use part of it as a shield, fastening it to his left arm with a few strips of spare tubing.

He emerged from the ship, not looking quite as impressive as Samus, but ready for battle nonetheless. "Now, try to keep up," Samus said, turning and running towards the northeast, and to whatever fate awaited them.

---------------------------------------------------------------------------  
_Meanwhile..._

"Sir, the Hunter is approaching from the south. And she has a companion," one of the Pirates said, approaching was no doubt their leader.

"I knew before you got here. Prepare a welcoming party for her," the commander said, in a low growling voice. "Alert me when she arrives," he said, spreading metallic wings, and taking off.

"C-commander Ridley?"

"I'll be preparing a surprise of my own for the Hunter," the dragon said, chuckling and soaring off into a deeper part of the facility.

-----------------------------------------------------------------------------

For some reason, Samus suddenly felt a chill run down her spine. Something didn't feel right, but she couldn't quite place her finger on it. She shook the distracting thoughts out of her mind, and checked to see if Maxis was still behind her. He was, and was managing to keep up with her. _Not too shabby. As long as he can keep it up, we'll be fine,_ she thought, continuing into the jungle, that strange feeling still nagging at her consciousness.

* * *

Well, that's chapter 3! I geuss now we just to have to wait to find out what kind of surprise Ridley has planned for Samus. 

That's all for now! Until next time!

Stay Snazzy!


	4. Chapter 4

That's right, folks! I have officially taken this off hiatus, and will be updating it regularly. Okay, so maybe regularly is a relative term. I'll be writing more of it, is what I'm trying to say.

* * *

**Chapter 4: Ambushed**

Samus skidded to a halt at the edge of the forest, her boots throwing up small chunks of earth and plant matter as they dug into the soft ground. Under her helmet, a smirk spread across her face. The ship's sensors were spot on, she thought to herself.

Stretching out for miles in either direction was the massive outer wall of a Pirate facility. Most of the wall was covered in ivy and other plants from the forest, and she was quite certain that several small animals had taken up residence in the shelter provided by the vegetation.

"Hey, why'y you- Oh," Maxis said, coming to a hlt next to the Hunter. "They don't do anything subtly, do they?" he remarked.

"They rarely do. Come on," Samus said, motioning for him to follow. She ran alongside the wall, using it as a guide to find exactly what she was looking for. Standing before them was a massive entry door, which was suspiciously unguarded. Something that bothered Samus, but she didn't dwell on it. The guards were probably further inside the base, guarding something important. They probably figured that no one would actually be able to get inside, and even if they did, the Pirates never kept the really important things in the open.

Sliding aside an dirt-encrusted panel revealed the security console that would allow those with proper authorisation access. Thanks to the technology of her suit, Samus ALWAYS had proper authorization, at least for the low-level security. Within a few seconds of interfacing with the machine, she had unlocked the door. There was a soft click, followed by a grinding sound as the door slid aside to grant access to the two. "That was easier than expected," Samus remarked. She shivered slightly as she felt a chill creep down her spine. Something was still bugging her about this, but she still couldn't figure out what it was. She walked a bit deeper into the facility, examining the lettering on several of the buildings.

"Let's hope it stays this easy," Maxis said, following the Hunter through the entryway. He cast a cautious glance at their surroundings. Nothing but empty space and storage warehouse, save a large tower peeking over the tops of the small buildings around it. "Where're the guards?" Maxis asked, as he finished surveying the area.

It was at this moment that everything seemed to fall into place. The lack of security, both inside the base, and on the entry software. The fact that they had not been swarmed by pirates the moment they set foot inside. That feeling that had been gnawing at her conciousness since they had set out. Everything had been all too easy up until this point, and Samus had finally realized why.

"Shit."

She whirled around to warn Maxis, only to find him fending off half a dozen assailants. "Sonuva-!" Just as she raised her arm cannon, she was struck from behind with enough force to knock her helmet clean off. It skidded across the ground, and out of reach. Samus lurched forward, feeling a hand to the back of her head. A trickle of warm liquid ran down her fingers. Her vision was blurred, and her body didn't seem to want to respond. She stumbled to the side, slamming her shoulder into the side of one of the warehouses, before tumbling to the ground. She fought to maintain conciousness, but couldn't shake away the fog creeping into her mind. As the world fell out from under her, she caught a glimpse of a cruel, jagged grin, and everything went black.

* * *

Yeah, it was short, but again, I tend to use short chapters to set up for longer ones. Anyways, keep reviewing, people! 

Until next time, you know what to do.

Stay Snazzy!


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